Ligand profile

NDN

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_02286 — Thymidylate synthase

Via homolog PDB 3b5b UniProt P0A884 Formula C₉H₁₂N₃O₁₀P
Mol. weight 353.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NDN
PDB
3b5b
UniProt (similar protein)
P0A884
Target protein
KP13_02286

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 353.18 Da
LogP (Crippen) -1.80
H-bond donors 4
H-bond acceptors 9
TPSA 194.22 Ų
Rotatable bonds 5
Aromatic rings 1 / 2
Heavy atoms 23
Fraction sp³ C 0.56
Formula C₉H₁₂N₃O₁₀P

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 194.2
  • −1 ≤ LogP ≤ 5 -1.80
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 353.2
  • LogP ≤ 5 -1.80
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 194.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O
InChI 
InChI=1S/C9H12N3O10P/c13-5-1-7(22-6(5)3-21-23(18,19)20)11-2-4(12(16)17)8(14)10-9(11)15/h2,5-7,13H,1,3H2,(H,10,14,15)(H2,18,19,20)/t5-,6+,7+/m0/s1
InChIKey 
LVLPVLNNXRTCHP-RRKCRQDMSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00303

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02286.

PDB 32

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)